In VS2010, the latest rev 5.3.4.1 of SQL prompt will not allow itself to be removed. I want to keep it in SSMS, but the startup check box is grayed out and checked. I can uncheck it as an available addin, but startup is not something I can change. I did check tools->environment setting, there are no references in add-ins. Any ideas?

Sorry you're having trouble with SQL Prompt. I think the first thing to do would be, try repairing the installation of SQL Prompt using Programs and features, then you should be capable of disabling the add-in in Visual Studio's add-in manager.

I've just figured out how to disable SQL Prompt in Visual Studio 2012.
Run VS as Administrator; hold down Ctrl and right click it, then select "Run as Administrator..." this should let you unselect the Start up check box.

Restart as normal and SQL Prompt is not enabled.

Works great for me. I Love SQL Prompt in SSMS (and do all my database work in there), Visual Studio (for me) is for .NET development and I don't really do any SQL work in the IDE so having it running just gets in my way at times.